Starting phenix.real_space_refine on Sun Sep 13 02:43:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vgn_21198/09_2026/6vgn_21198.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vgn_21198/09_2026/6vgn_21198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vgn_21198/09_2026/6vgn_21198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vgn_21198/09_2026/6vgn_21198.map" model { file = "/net/cci-nas-00/data/ceres_data/6vgn_21198/09_2026/6vgn_21198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vgn_21198/09_2026/6vgn_21198.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6vgn_21198/09_2026/6vgn_21198.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vgn_21198/09_2026/6vgn_21198.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.360 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 119 5.16 5 C 12922 2.51 5 N 3444 2.21 5 O 3948 1.98 5 F 14 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20447 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1508 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "H" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1357 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain: "V" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 56 Unusual residues: {'R0M': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 2, None: 1} Not linked: pdbres="R0M V 1 " pdbres="WFP V 2 " Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'R0M:plan-1': 1, 'WFP:plan-2': 1, 'ALO:plan-1': 1, 'YCP:plan-1': 1, 'MP8:plan-1': 1} Unresolved non-hydrogen planarities: 5 Restraints were copied for chains: B, C, D, E, F, G, I, J, K, L, M, N, W, X, Y, Z, a, b Time building chain proxies: 2.70, per 1000 atoms: 0.13 Number of scatterers: 20447 At special positions: 0 Unit cell: (115.54, 115.54, 117.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 119 16.00 F 14 9.00 O 3948 8.00 N 3444 7.00 C 12922 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=14, symmetry=0 Number of additional bonds: simple=14, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 793.3 milliseconds 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4956 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 35 sheets defined 50.3% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 49 through 67 removed outlier: 3.938A pdb=" N ASP A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 110 through 118 removed outlier: 3.761A pdb=" N VAL A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 173 removed outlier: 4.283A pdb=" N ALA A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'B' and resid 33 through 39 Processing helix chain 'B' and resid 49 through 67 removed outlier: 3.938A pdb=" N ASP B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 96 Processing helix chain 'B' and resid 110 through 118 removed outlier: 3.761A pdb=" N VAL B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 173 removed outlier: 4.284A pdb=" N ALA B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'C' and resid 33 through 39 Processing helix chain 'C' and resid 49 through 67 removed outlier: 3.938A pdb=" N ASP C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 96 Processing helix chain 'C' and resid 110 through 118 removed outlier: 3.760A pdb=" N VAL C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 173 removed outlier: 4.283A pdb=" N ALA C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'D' and resid 33 through 39 Processing helix chain 'D' and resid 49 through 67 removed outlier: 3.938A pdb=" N ASP D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 96 Processing helix chain 'D' and resid 110 through 118 removed outlier: 3.761A pdb=" N VAL D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 173 removed outlier: 4.283A pdb=" N ALA D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'E' and resid 33 through 39 Processing helix chain 'E' and resid 49 through 67 removed outlier: 3.938A pdb=" N ASP E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 96 Processing helix chain 'E' and resid 110 through 118 removed outlier: 3.761A pdb=" N VAL E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 173 removed outlier: 4.283A pdb=" N ALA E 154 " --> pdb=" O LEU E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 184 Processing helix chain 'E' and resid 192 through 197 Processing helix chain 'F' and resid 33 through 39 Processing helix chain 'F' and resid 49 through 67 removed outlier: 3.937A pdb=" N ASP F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 96 Processing helix chain 'F' and resid 110 through 118 removed outlier: 3.760A pdb=" N VAL F 114 " --> pdb=" O SER F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 173 removed outlier: 4.283A pdb=" N ALA F 154 " --> pdb=" O LEU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 184 Processing helix chain 'F' and resid 192 through 197 Processing helix chain 'G' and resid 33 through 39 Processing helix chain 'G' and resid 49 through 67 removed outlier: 3.938A pdb=" N ASP G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 96 Processing helix chain 'G' and resid 110 through 118 removed outlier: 3.761A pdb=" N VAL G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 173 removed outlier: 4.283A pdb=" N ALA G 154 " --> pdb=" O LEU G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 184 Processing helix chain 'G' and resid 192 through 197 Processing helix chain 'H' and resid 16 through 26 Processing helix chain 'H' and resid 37 through 55 Processing helix chain 'H' and resid 70 through 84 Processing helix chain 'H' and resid 98 through 106 Processing helix chain 'H' and resid 132 through 159 removed outlier: 3.900A pdb=" N ILE H 138 " --> pdb=" O ALA H 134 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU H 141 " --> pdb=" O ALA H 137 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 170 Processing helix chain 'H' and resid 177 through 183 Processing helix chain 'I' and resid 16 through 26 Processing helix chain 'I' and resid 37 through 55 Processing helix chain 'I' and resid 70 through 84 Processing helix chain 'I' and resid 98 through 106 Processing helix chain 'I' and resid 132 through 159 removed outlier: 3.900A pdb=" N ILE I 138 " --> pdb=" O ALA I 134 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU I 141 " --> pdb=" O ALA I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 170 Processing helix chain 'I' and resid 177 through 183 Processing helix chain 'J' and resid 16 through 26 Processing helix chain 'J' and resid 37 through 55 Processing helix chain 'J' and resid 70 through 84 Processing helix chain 'J' and resid 98 through 106 Processing helix chain 'J' and resid 132 through 159 removed outlier: 3.899A pdb=" N ILE J 138 " --> pdb=" O ALA J 134 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU J 141 " --> pdb=" O ALA J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 170 Processing helix chain 'J' and resid 177 through 183 Processing helix chain 'K' and resid 16 through 26 Processing helix chain 'K' and resid 37 through 55 Processing helix chain 'K' and resid 70 through 84 Processing helix chain 'K' and resid 98 through 106 Processing helix chain 'K' and resid 132 through 159 removed outlier: 3.900A pdb=" N ILE K 138 " --> pdb=" O ALA K 134 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU K 141 " --> pdb=" O ALA K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 170 Processing helix chain 'K' and resid 177 through 183 Processing helix chain 'L' and resid 16 through 26 Processing helix chain 'L' and resid 37 through 55 Processing helix chain 'L' and resid 70 through 84 Processing helix chain 'L' and resid 98 through 106 Processing helix chain 'L' and resid 132 through 159 removed outlier: 3.900A pdb=" N ILE L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU L 141 " --> pdb=" O ALA L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 170 Processing helix chain 'L' and resid 177 through 183 Processing helix chain 'M' and resid 16 through 26 Processing helix chain 'M' and resid 37 through 55 Processing helix chain 'M' and resid 70 through 84 Processing helix chain 'M' and resid 98 through 106 Processing helix chain 'M' and resid 132 through 159 removed outlier: 3.900A pdb=" N ILE M 138 " --> pdb=" O ALA M 134 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU M 141 " --> pdb=" O ALA M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 170 Processing helix chain 'M' and resid 177 through 183 Processing helix chain 'N' and resid 16 through 26 Processing helix chain 'N' and resid 37 through 55 Processing helix chain 'N' and resid 70 through 84 Processing helix chain 'N' and resid 98 through 106 Processing helix chain 'N' and resid 132 through 159 removed outlier: 3.900A pdb=" N ILE N 138 " --> pdb=" O ALA N 134 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU N 141 " --> pdb=" O ALA N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 170 Processing helix chain 'N' and resid 177 through 183 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 44 removed outlier: 5.242A pdb=" N SER A 78 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN A 107 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG A 131 " --> pdb=" O CYS A 104 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLY A 106 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N LEU A 133 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA A 108 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 44 removed outlier: 5.242A pdb=" N SER A 78 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN A 107 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N MET A 125 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N THR A 102 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 19 through 23 Processing sheet with id=AA5, first strand: chain 'B' and resid 41 through 44 removed outlier: 5.242A pdb=" N SER B 78 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN B 107 " --> pdb=" O SER B 78 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ARG B 131 " --> pdb=" O CYS B 104 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY B 106 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU B 133 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 41 through 44 removed outlier: 5.242A pdb=" N SER B 78 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN B 107 " --> pdb=" O SER B 78 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N MET B 125 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N THR B 102 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 19 through 23 Processing sheet with id=AA8, first strand: chain 'C' and resid 41 through 44 removed outlier: 5.243A pdb=" N SER C 78 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN C 107 " --> pdb=" O SER C 78 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ARG C 131 " --> pdb=" O CYS C 104 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY C 106 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU C 133 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA C 108 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 41 through 44 removed outlier: 5.243A pdb=" N SER C 78 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN C 107 " --> pdb=" O SER C 78 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N MET C 125 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N THR C 102 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 19 through 23 Processing sheet with id=AB2, first strand: chain 'D' and resid 41 through 44 removed outlier: 5.243A pdb=" N SER D 78 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN D 107 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG D 131 " --> pdb=" O CYS D 104 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY D 106 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU D 133 " --> pdb=" O GLY D 106 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA D 108 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 41 through 44 removed outlier: 5.243A pdb=" N SER D 78 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN D 107 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N MET D 125 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N THR D 102 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 19 through 23 Processing sheet with id=AB5, first strand: chain 'E' and resid 41 through 44 removed outlier: 5.242A pdb=" N SER E 78 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN E 107 " --> pdb=" O SER E 78 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ARG E 131 " --> pdb=" O CYS E 104 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY E 106 " --> pdb=" O ARG E 131 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU E 133 " --> pdb=" O GLY E 106 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA E 108 " --> pdb=" O LEU E 133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 41 through 44 removed outlier: 5.242A pdb=" N SER E 78 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLN E 107 " --> pdb=" O SER E 78 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N MET E 125 " --> pdb=" O ILE E 100 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N THR E 102 " --> pdb=" O MET E 125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 19 through 23 Processing sheet with id=AB8, first strand: chain 'F' and resid 41 through 44 removed outlier: 5.242A pdb=" N SER F 78 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLN F 107 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG F 131 " --> pdb=" O CYS F 104 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY F 106 " --> pdb=" O ARG F 131 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N LEU F 133 " --> pdb=" O GLY F 106 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA F 108 " --> pdb=" O LEU F 133 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 41 through 44 removed outlier: 5.242A pdb=" N SER F 78 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLN F 107 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N MET F 125 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N THR F 102 " --> pdb=" O MET F 125 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 19 through 23 Processing sheet with id=AC2, first strand: chain 'G' and resid 41 through 44 removed outlier: 5.242A pdb=" N SER G 78 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLN G 107 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG G 131 " --> pdb=" O CYS G 104 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY G 106 " --> pdb=" O ARG G 131 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU G 133 " --> pdb=" O GLY G 106 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA G 108 " --> pdb=" O LEU G 133 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 41 through 44 removed outlier: 5.242A pdb=" N SER G 78 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLN G 107 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N MET G 125 " --> pdb=" O ILE G 100 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N THR G 102 " --> pdb=" O MET G 125 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 29 through 32 removed outlier: 6.588A pdb=" N ILE H 30 " --> pdb=" O TYR H 63 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN H 65 " --> pdb=" O ILE H 30 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU H 32 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER H 66 " --> pdb=" O MET H 93 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N MET H 95 " --> pdb=" O SER H 66 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ARG H 119 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLY H 94 " --> pdb=" O ARG H 119 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU H 121 " --> pdb=" O GLY H 94 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA H 96 " --> pdb=" O LEU H 121 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N MET H 122 " --> pdb=" O ARG H 173 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ARG H 173 " --> pdb=" O MET H 122 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 29 through 32 removed outlier: 6.588A pdb=" N ILE H 30 " --> pdb=" O TYR H 63 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN H 65 " --> pdb=" O ILE H 30 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU H 32 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER H 66 " --> pdb=" O MET H 93 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N MET H 95 " --> pdb=" O SER H 66 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N TYR H 113 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR H 90 " --> pdb=" O TYR H 113 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 29 through 32 removed outlier: 6.587A pdb=" N ILE I 30 " --> pdb=" O TYR I 63 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN I 65 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU I 32 " --> pdb=" O ASN I 65 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N SER I 66 " --> pdb=" O MET I 93 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N MET I 95 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG I 119 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLY I 94 " --> pdb=" O ARG I 119 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU I 121 " --> pdb=" O GLY I 94 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA I 96 " --> pdb=" O LEU I 121 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET I 122 " --> pdb=" O ARG I 173 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ARG I 173 " --> pdb=" O MET I 122 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 29 through 32 removed outlier: 6.587A pdb=" N ILE I 30 " --> pdb=" O TYR I 63 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN I 65 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU I 32 " --> pdb=" O ASN I 65 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N SER I 66 " --> pdb=" O MET I 93 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N MET I 95 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N TYR I 113 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR I 90 " --> pdb=" O TYR I 113 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 29 through 32 removed outlier: 6.588A pdb=" N ILE J 30 " --> pdb=" O TYR J 63 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN J 65 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU J 32 " --> pdb=" O ASN J 65 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER J 66 " --> pdb=" O MET J 93 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N MET J 95 " --> pdb=" O SER J 66 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ARG J 119 " --> pdb=" O ALA J 92 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLY J 94 " --> pdb=" O ARG J 119 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU J 121 " --> pdb=" O GLY J 94 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA J 96 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N MET J 122 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG J 173 " --> pdb=" O MET J 122 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 29 through 32 removed outlier: 6.588A pdb=" N ILE J 30 " --> pdb=" O TYR J 63 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN J 65 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU J 32 " --> pdb=" O ASN J 65 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER J 66 " --> pdb=" O MET J 93 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N MET J 95 " --> pdb=" O SER J 66 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N TYR J 113 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR J 90 " --> pdb=" O TYR J 113 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 29 through 32 removed outlier: 6.587A pdb=" N ILE K 30 " --> pdb=" O TYR K 63 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN K 65 " --> pdb=" O ILE K 30 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU K 32 " --> pdb=" O ASN K 65 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER K 66 " --> pdb=" O MET K 93 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N MET K 95 " --> pdb=" O SER K 66 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG K 119 " --> pdb=" O ALA K 92 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLY K 94 " --> pdb=" O ARG K 119 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU K 121 " --> pdb=" O GLY K 94 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA K 96 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET K 122 " --> pdb=" O ARG K 173 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ARG K 173 " --> pdb=" O MET K 122 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 29 through 32 removed outlier: 6.587A pdb=" N ILE K 30 " --> pdb=" O TYR K 63 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN K 65 " --> pdb=" O ILE K 30 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU K 32 " --> pdb=" O ASN K 65 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER K 66 " --> pdb=" O MET K 93 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N MET K 95 " --> pdb=" O SER K 66 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N TYR K 113 " --> pdb=" O ILE K 88 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR K 90 " --> pdb=" O TYR K 113 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 29 through 32 removed outlier: 6.588A pdb=" N ILE L 30 " --> pdb=" O TYR L 63 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN L 65 " --> pdb=" O ILE L 30 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU L 32 " --> pdb=" O ASN L 65 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N SER L 66 " --> pdb=" O MET L 93 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N MET L 95 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG L 119 " --> pdb=" O ALA L 92 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLY L 94 " --> pdb=" O ARG L 119 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU L 121 " --> pdb=" O GLY L 94 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA L 96 " --> pdb=" O LEU L 121 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET L 122 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ARG L 173 " --> pdb=" O MET L 122 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 29 through 32 removed outlier: 6.588A pdb=" N ILE L 30 " --> pdb=" O TYR L 63 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN L 65 " --> pdb=" O ILE L 30 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU L 32 " --> pdb=" O ASN L 65 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N SER L 66 " --> pdb=" O MET L 93 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N MET L 95 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N TYR L 113 " --> pdb=" O ILE L 88 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR L 90 " --> pdb=" O TYR L 113 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.587A pdb=" N ILE M 30 " --> pdb=" O TYR M 63 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN M 65 " --> pdb=" O ILE M 30 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU M 32 " --> pdb=" O ASN M 65 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER M 66 " --> pdb=" O MET M 93 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N MET M 95 " --> pdb=" O SER M 66 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG M 119 " --> pdb=" O ALA M 92 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLY M 94 " --> pdb=" O ARG M 119 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU M 121 " --> pdb=" O GLY M 94 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA M 96 " --> pdb=" O LEU M 121 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N MET M 122 " --> pdb=" O ARG M 173 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG M 173 " --> pdb=" O MET M 122 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.587A pdb=" N ILE M 30 " --> pdb=" O TYR M 63 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN M 65 " --> pdb=" O ILE M 30 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU M 32 " --> pdb=" O ASN M 65 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER M 66 " --> pdb=" O MET M 93 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N MET M 95 " --> pdb=" O SER M 66 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N TYR M 113 " --> pdb=" O ILE M 88 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR M 90 " --> pdb=" O TYR M 113 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.588A pdb=" N ILE N 30 " --> pdb=" O TYR N 63 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN N 65 " --> pdb=" O ILE N 30 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU N 32 " --> pdb=" O ASN N 65 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER N 66 " --> pdb=" O MET N 93 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N MET N 95 " --> pdb=" O SER N 66 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ARG N 119 " --> pdb=" O ALA N 92 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLY N 94 " --> pdb=" O ARG N 119 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LEU N 121 " --> pdb=" O GLY N 94 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA N 96 " --> pdb=" O LEU N 121 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET N 122 " --> pdb=" O ARG N 173 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ARG N 173 " --> pdb=" O MET N 122 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.588A pdb=" N ILE N 30 " --> pdb=" O TYR N 63 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ASN N 65 " --> pdb=" O ILE N 30 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU N 32 " --> pdb=" O ASN N 65 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER N 66 " --> pdb=" O MET N 93 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N MET N 95 " --> pdb=" O SER N 66 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N TYR N 113 " --> pdb=" O ILE N 88 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR N 90 " --> pdb=" O TYR N 113 " (cutoff:3.500A) 1204 hydrogen bonds defined for protein. 3528 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.91 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4123 1.31 - 1.44: 5408 1.44 - 1.57: 10971 1.57 - 1.70: 43 1.70 - 1.83: 217 Bond restraints: 20762 Sorted by residual: bond pdb=" N MP8 X 7 " pdb=" CA MP8 X 7 " ideal model delta sigma weight residual 1.466 1.312 0.154 1.50e-02 4.44e+03 1.06e+02 bond pdb=" N MP8 b 7 " pdb=" CA MP8 b 7 " ideal model delta sigma weight residual 1.466 1.312 0.154 1.50e-02 4.44e+03 1.05e+02 bond pdb=" N MP8 Z 7 " pdb=" CA MP8 Z 7 " ideal model delta sigma weight residual 1.466 1.312 0.154 1.50e-02 4.44e+03 1.05e+02 bond pdb=" N MP8 V 7 " pdb=" CA MP8 V 7 " ideal model delta sigma weight residual 1.466 1.312 0.154 1.50e-02 4.44e+03 1.05e+02 bond pdb=" N MP8 W 7 " pdb=" CA MP8 W 7 " ideal model delta sigma weight residual 1.466 1.312 0.154 1.50e-02 4.44e+03 1.05e+02 ... (remaining 20757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 26226 3.40 - 6.80: 1744 6.80 - 10.20: 58 10.20 - 13.60: 28 13.60 - 17.00: 7 Bond angle restraints: 28063 Sorted by residual: angle pdb=" C MP8 a 7 " pdb=" CA MP8 a 7 " pdb=" CB MP8 a 7 " ideal model delta sigma weight residual 110.10 127.10 -17.00 1.90e+00 2.77e-01 8.01e+01 angle pdb=" C MP8 Y 7 " pdb=" CA MP8 Y 7 " pdb=" CB MP8 Y 7 " ideal model delta sigma weight residual 110.10 127.10 -17.00 1.90e+00 2.77e-01 8.00e+01 angle pdb=" C MP8 W 7 " pdb=" CA MP8 W 7 " pdb=" CB MP8 W 7 " ideal model delta sigma weight residual 110.10 127.07 -16.97 1.90e+00 2.77e-01 7.98e+01 angle pdb=" C MP8 V 7 " pdb=" CA MP8 V 7 " pdb=" CB MP8 V 7 " ideal model delta sigma weight residual 110.10 127.06 -16.96 1.90e+00 2.77e-01 7.97e+01 angle pdb=" C MP8 b 7 " pdb=" CA MP8 b 7 " pdb=" CB MP8 b 7 " ideal model delta sigma weight residual 110.10 127.06 -16.96 1.90e+00 2.77e-01 7.97e+01 ... (remaining 28058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.31: 12334 24.31 - 48.62: 203 48.62 - 72.93: 49 72.93 - 97.24: 21 97.24 - 121.56: 7 Dihedral angle restraints: 12614 sinusoidal: 4935 harmonic: 7679 Sorted by residual: dihedral pdb=" C MP8 b 7 " pdb=" N MP8 b 7 " pdb=" CA MP8 b 7 " pdb=" CB MP8 b 7 " ideal model delta harmonic sigma weight residual -122.60 -170.85 48.25 0 2.50e+00 1.60e-01 3.73e+02 dihedral pdb=" C MP8 W 7 " pdb=" N MP8 W 7 " pdb=" CA MP8 W 7 " pdb=" CB MP8 W 7 " ideal model delta harmonic sigma weight residual -122.60 -170.83 48.23 0 2.50e+00 1.60e-01 3.72e+02 dihedral pdb=" C MP8 X 7 " pdb=" N MP8 X 7 " pdb=" CA MP8 X 7 " pdb=" CB MP8 X 7 " ideal model delta harmonic sigma weight residual -122.60 -170.81 48.21 0 2.50e+00 1.60e-01 3.72e+02 ... (remaining 12611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.480: 3241 0.480 - 0.961: 0 0.961 - 1.441: 0 1.441 - 1.921: 0 1.921 - 2.402: 7 Chirality restraints: 3248 Sorted by residual: chirality pdb=" CA MP8 b 7 " pdb=" N MP8 b 7 " pdb=" C MP8 b 7 " pdb=" CB MP8 b 7 " both_signs ideal model delta sigma weight residual False 2.72 0.32 2.40 2.00e-01 2.50e+01 1.44e+02 chirality pdb=" CA MP8 W 7 " pdb=" N MP8 W 7 " pdb=" C MP8 W 7 " pdb=" CB MP8 W 7 " both_signs ideal model delta sigma weight residual False 2.72 0.32 2.40 2.00e-01 2.50e+01 1.44e+02 chirality pdb=" CA MP8 X 7 " pdb=" N MP8 X 7 " pdb=" C MP8 X 7 " pdb=" CB MP8 X 7 " both_signs ideal model delta sigma weight residual False 2.72 0.32 2.40 2.00e-01 2.50e+01 1.44e+02 ... (remaining 3245 not shown) Planarity restraints: 3640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 149 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C ASP E 149 " -0.056 2.00e-02 2.50e+03 pdb=" O ASP E 149 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU E 150 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 149 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C ASP C 149 " -0.056 2.00e-02 2.50e+03 pdb=" O ASP C 149 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU C 150 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 149 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C ASP B 149 " 0.056 2.00e-02 2.50e+03 pdb=" O ASP B 149 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU B 150 " -0.019 2.00e-02 2.50e+03 ... (remaining 3637 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 8682 2.90 - 3.40: 20650 3.40 - 3.90: 36080 3.90 - 4.40: 42999 4.40 - 4.90: 67943 Nonbonded interactions: 176354 Sorted by model distance: nonbonded pdb=" N PRO E 32 " pdb=" O PRO E 32 " model vdw 2.401 2.496 nonbonded pdb=" N PRO B 32 " pdb=" O PRO B 32 " model vdw 2.401 2.496 nonbonded pdb=" N PRO A 32 " pdb=" O PRO A 32 " model vdw 2.401 2.496 nonbonded pdb=" N PRO D 32 " pdb=" O PRO D 32 " model vdw 2.401 2.496 nonbonded pdb=" N PRO G 32 " pdb=" O PRO G 32 " model vdw 2.401 2.496 ... (remaining 176349 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 17.430 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 0.213 20776 Z= 1.127 Angle : 1.786 17.003 28063 Z= 1.172 Chirality : 0.141 2.402 3248 Planarity : 0.009 0.040 3640 Dihedral : 11.331 121.555 7658 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.15), residues: 2590 helix: -0.38 (0.12), residues: 1358 sheet: 2.07 (0.31), residues: 231 loop : 0.36 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 124 TYR 0.038 0.008 TYR N 183 PHE 0.022 0.004 PHE D 43 TRP 0.007 0.004 TRP L 174 HIS 0.010 0.003 HIS I 123 Details of bonding type rmsd/Z covalent geometry : bond 0.02090 / 1.11 (20762) covalent geometry : angle 1.78604 / 1.17 (28063) hydrogen bonds : bond 0.16131 / 10.75 ( 1106) hydrogen bonds : angle 7.12939 / 5.06 ( 3528) Misc. bond : bond 0.08146 / 4.59 ( 14) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 0.741 Fit side-chains REVERT: A 21 GLU cc_start: 0.8015 (tt0) cc_final: 0.7114 (pt0) REVERT: A 164 MET cc_start: 0.6760 (ttm) cc_final: 0.6526 (ttt) REVERT: A 175 ASP cc_start: 0.7455 (t70) cc_final: 0.7217 (m-30) REVERT: B 21 GLU cc_start: 0.7723 (tt0) cc_final: 0.7047 (pt0) REVERT: B 25 PHE cc_start: 0.5660 (m-10) cc_final: 0.5370 (m-80) REVERT: B 135 HIS cc_start: 0.6670 (m-70) cc_final: 0.6444 (m170) REVERT: B 164 MET cc_start: 0.6959 (ttm) cc_final: 0.6565 (ttt) REVERT: B 175 ASP cc_start: 0.7556 (t70) cc_final: 0.7194 (m-30) REVERT: C 21 GLU cc_start: 0.7347 (tt0) cc_final: 0.7034 (pt0) REVERT: C 135 HIS cc_start: 0.6446 (m-70) cc_final: 0.6100 (m-70) REVERT: C 164 MET cc_start: 0.6904 (ttm) cc_final: 0.6570 (ttt) REVERT: C 175 ASP cc_start: 0.7664 (t70) cc_final: 0.6878 (m-30) REVERT: D 164 MET cc_start: 0.6615 (ttm) cc_final: 0.6241 (ttt) REVERT: D 190 THR cc_start: 0.8332 (p) cc_final: 0.7975 (t) REVERT: E 21 GLU cc_start: 0.7310 (tt0) cc_final: 0.6957 (pt0) REVERT: E 164 MET cc_start: 0.6483 (ttm) cc_final: 0.6117 (ttt) REVERT: F 21 GLU cc_start: 0.7898 (tt0) cc_final: 0.7157 (pt0) REVERT: F 95 TYR cc_start: 0.8138 (t80) cc_final: 0.7915 (t80) REVERT: F 164 MET cc_start: 0.6634 (ttm) cc_final: 0.6249 (ttt) REVERT: G 164 MET cc_start: 0.7029 (ttm) cc_final: 0.6675 (ttt) REVERT: G 175 ASP cc_start: 0.7464 (t70) cc_final: 0.6848 (m-30) REVERT: G 200 ILE cc_start: 0.8180 (mm) cc_final: 0.7971 (mt) REVERT: H 70 SER cc_start: 0.7951 (m) cc_final: 0.7720 (p) REVERT: H 150 MET cc_start: 0.7473 (ttt) cc_final: 0.7068 (ttt) REVERT: H 179 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8325 (mt-10) REVERT: I 70 SER cc_start: 0.8154 (m) cc_final: 0.7807 (p) REVERT: I 75 MET cc_start: 0.8296 (mmt) cc_final: 0.7868 (mmp) REVERT: J 39 GLU cc_start: 0.7176 (tp30) cc_final: 0.6975 (tp30) REVERT: J 70 SER cc_start: 0.8173 (m) cc_final: 0.7889 (p) REVERT: J 166 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8260 (mt-10) REVERT: J 179 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8176 (mt-10) REVERT: K 75 MET cc_start: 0.8426 (mmt) cc_final: 0.8129 (tpp) REVERT: L 158 THR cc_start: 0.8268 (p) cc_final: 0.8054 (p) REVERT: L 163 GLU cc_start: 0.8364 (mp0) cc_final: 0.7685 (pm20) REVERT: M 79 ASP cc_start: 0.8229 (m-30) cc_final: 0.7992 (m-30) REVERT: M 163 GLU cc_start: 0.8287 (mp0) cc_final: 0.7809 (pm20) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.1517 time to fit residues: 107.5450 Evaluate side-chains 312 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.145885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.122770 restraints weight = 23592.823| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.17 r_work: 0.3267 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20776 Z= 0.178 Angle : 0.639 7.090 28063 Z= 0.338 Chirality : 0.043 0.166 3248 Planarity : 0.004 0.031 3640 Dihedral : 8.730 102.138 2933 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.99 % Allowed : 4.20 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.16), residues: 2590 helix: 1.27 (0.14), residues: 1372 sheet: 3.22 (0.29), residues: 245 loop : -0.36 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 97 TYR 0.013 0.002 TYR M 21 PHE 0.014 0.002 PHE K 175 TRP 0.007 0.001 TRP M 174 HIS 0.005 0.001 HIS C 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (20762) covalent geometry : angle 0.63929 / 0.34 (28063) hydrogen bonds : bond 0.03858 / 2.61 ( 1106) hydrogen bonds : angle 4.78690 / 3.33 ( 3528) Misc. bond : bond 0.00153 / 0.09 ( 14) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 434 time to evaluate : 0.747 Fit side-chains REVERT: A 164 MET cc_start: 0.7330 (ttm) cc_final: 0.6954 (ttt) REVERT: A 175 ASP cc_start: 0.7599 (t70) cc_final: 0.7055 (m-30) REVERT: B 125 MET cc_start: 0.8964 (mtm) cc_final: 0.8756 (mtm) REVERT: B 164 MET cc_start: 0.7545 (ttm) cc_final: 0.7108 (ttt) REVERT: B 175 ASP cc_start: 0.7608 (t70) cc_final: 0.7122 (m-30) REVERT: C 164 MET cc_start: 0.7434 (ttm) cc_final: 0.7039 (ttt) REVERT: C 175 ASP cc_start: 0.7496 (t70) cc_final: 0.6752 (m-30) REVERT: D 74 MET cc_start: 0.8712 (ttm) cc_final: 0.8438 (mtp) REVERT: D 93 MET cc_start: 0.8526 (mtp) cc_final: 0.8197 (mtp) REVERT: D 164 MET cc_start: 0.7265 (ttm) cc_final: 0.6900 (ttt) REVERT: E 21 GLU cc_start: 0.8188 (tt0) cc_final: 0.7843 (pt0) REVERT: E 135 HIS cc_start: 0.7884 (t-170) cc_final: 0.7520 (t-170) REVERT: E 164 MET cc_start: 0.7428 (ttm) cc_final: 0.7041 (ttt) REVERT: F 21 GLU cc_start: 0.8238 (tt0) cc_final: 0.7787 (pt0) REVERT: F 93 MET cc_start: 0.8440 (mtp) cc_final: 0.8051 (mtp) REVERT: F 97 ARG cc_start: 0.7693 (mpt180) cc_final: 0.7400 (mpt180) REVERT: F 164 MET cc_start: 0.7311 (ttm) cc_final: 0.6921 (ttt) REVERT: F 200 ILE cc_start: 0.8444 (mm) cc_final: 0.8175 (mt) REVERT: G 164 MET cc_start: 0.7563 (ttm) cc_final: 0.7140 (ttt) REVERT: G 175 ASP cc_start: 0.7484 (t70) cc_final: 0.6808 (m-30) REVERT: H 22 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7880 (tm-30) REVERT: H 150 MET cc_start: 0.8058 (ttt) cc_final: 0.7601 (ttt) REVERT: H 158 THR cc_start: 0.8528 (p) cc_final: 0.8276 (p) REVERT: H 183 TYR cc_start: 0.8455 (t80) cc_final: 0.8051 (t80) REVERT: I 75 MET cc_start: 0.8235 (mmt) cc_final: 0.7901 (mmp) REVERT: I 79 ASP cc_start: 0.8024 (m-30) cc_final: 0.7739 (m-30) REVERT: I 109 LYS cc_start: 0.8443 (mttp) cc_final: 0.8174 (mmtm) REVERT: I 183 TYR cc_start: 0.8342 (t80) cc_final: 0.8097 (t80) REVERT: J 166 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7600 (mt-10) REVERT: J 183 TYR cc_start: 0.8530 (t80) cc_final: 0.8289 (t80) REVERT: K 150 MET cc_start: 0.7882 (ttt) cc_final: 0.7557 (ttt) REVERT: K 163 GLU cc_start: 0.8132 (mp0) cc_final: 0.7589 (pm20) REVERT: K 183 TYR cc_start: 0.8471 (t80) cc_final: 0.8093 (t80) REVERT: L 158 THR cc_start: 0.8426 (p) cc_final: 0.8199 (p) REVERT: L 163 GLU cc_start: 0.8439 (mp0) cc_final: 0.7684 (pm20) REVERT: L 182 GLU cc_start: 0.8588 (tp30) cc_final: 0.8359 (tp30) REVERT: M 75 MET cc_start: 0.8434 (tpp) cc_final: 0.8126 (mmt) REVERT: M 109 LYS cc_start: 0.8369 (mttp) cc_final: 0.8121 (mmtm) REVERT: M 163 GLU cc_start: 0.8376 (mp0) cc_final: 0.7715 (pm20) REVERT: N 183 TYR cc_start: 0.8442 (t80) cc_final: 0.8216 (t80) outliers start: 21 outliers final: 10 residues processed: 446 average time/residue: 0.1610 time to fit residues: 108.9824 Evaluate side-chains 355 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 345 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain N residue 70 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 115 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 221 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 199 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 186 optimal weight: 0.4980 chunk 162 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 77 ASN F 129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.149398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.125695 restraints weight = 23500.186| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.27 r_work: 0.3315 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 20776 Z= 0.118 Angle : 0.554 7.972 28063 Z= 0.285 Chirality : 0.041 0.171 3248 Planarity : 0.004 0.035 3640 Dihedral : 7.933 106.862 2933 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.13 % Allowed : 7.50 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.16), residues: 2590 helix: 1.69 (0.14), residues: 1379 sheet: 2.70 (0.29), residues: 245 loop : -0.40 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 23 TYR 0.019 0.001 TYR F 197 PHE 0.010 0.001 PHE L 185 TRP 0.005 0.001 TRP M 174 HIS 0.005 0.001 HIS D 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (20762) covalent geometry : angle 0.55356 / 0.29 (28063) hydrogen bonds : bond 0.03144 / 2.14 ( 1106) hydrogen bonds : angle 4.29047 / 2.98 ( 3528) Misc. bond : bond 0.00038 / 0.02 ( 14) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 395 time to evaluate : 0.783 Fit side-chains REVERT: A 135 HIS cc_start: 0.6735 (m170) cc_final: 0.6430 (m170) REVERT: A 164 MET cc_start: 0.7230 (ttm) cc_final: 0.6838 (ttt) REVERT: A 175 ASP cc_start: 0.7368 (t70) cc_final: 0.7087 (m-30) REVERT: B 50 ASP cc_start: 0.6971 (t70) cc_final: 0.6741 (t70) REVERT: B 164 MET cc_start: 0.7355 (ttm) cc_final: 0.6939 (ttt) REVERT: B 175 ASP cc_start: 0.7498 (t70) cc_final: 0.6964 (m-30) REVERT: C 164 MET cc_start: 0.7302 (ttm) cc_final: 0.6917 (ttt) REVERT: C 175 ASP cc_start: 0.7553 (t70) cc_final: 0.6791 (m-30) REVERT: D 74 MET cc_start: 0.8714 (ttm) cc_final: 0.8502 (mtp) REVERT: D 93 MET cc_start: 0.8449 (mtp) cc_final: 0.8170 (mtp) REVERT: D 135 HIS cc_start: 0.7336 (t-170) cc_final: 0.7115 (t-170) REVERT: D 164 MET cc_start: 0.7262 (ttm) cc_final: 0.6848 (ttt) REVERT: D 175 ASP cc_start: 0.7076 (t70) cc_final: 0.6562 (m-30) REVERT: E 135 HIS cc_start: 0.7573 (t-170) cc_final: 0.7347 (t-170) REVERT: E 164 MET cc_start: 0.7167 (ttm) cc_final: 0.6812 (ttt) REVERT: F 93 MET cc_start: 0.8319 (mtp) cc_final: 0.7946 (mtp) REVERT: F 135 HIS cc_start: 0.7684 (t-170) cc_final: 0.7366 (t-170) REVERT: F 164 MET cc_start: 0.7066 (ttm) cc_final: 0.6748 (ttt) REVERT: F 175 ASP cc_start: 0.7493 (t70) cc_final: 0.6866 (m-30) REVERT: G 164 MET cc_start: 0.7349 (ttm) cc_final: 0.6933 (ttt) REVERT: G 175 ASP cc_start: 0.7416 (t70) cc_final: 0.6793 (m-30) REVERT: H 150 MET cc_start: 0.7989 (ttt) cc_final: 0.7551 (ttt) REVERT: H 158 THR cc_start: 0.8413 (p) cc_final: 0.8166 (p) REVERT: H 163 GLU cc_start: 0.8033 (mp0) cc_final: 0.7548 (pm20) REVERT: H 183 TYR cc_start: 0.8402 (t80) cc_final: 0.8099 (t80) REVERT: I 75 MET cc_start: 0.8383 (mmt) cc_final: 0.8096 (mmp) REVERT: I 173 ARG cc_start: 0.7429 (ttt180) cc_final: 0.7223 (ptm160) REVERT: J 166 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7748 (mt-10) REVERT: J 183 TYR cc_start: 0.8483 (t80) cc_final: 0.8272 (t80) REVERT: K 150 MET cc_start: 0.7816 (ttt) cc_final: 0.7562 (ttt) REVERT: K 163 GLU cc_start: 0.8167 (mp0) cc_final: 0.7650 (pm20) REVERT: L 158 THR cc_start: 0.8377 (p) cc_final: 0.8130 (p) REVERT: L 163 GLU cc_start: 0.8493 (mp0) cc_final: 0.7710 (pm20) REVERT: L 183 TYR cc_start: 0.8446 (t80) cc_final: 0.8234 (t80) REVERT: M 75 MET cc_start: 0.8311 (tpp) cc_final: 0.8075 (mmt) REVERT: M 163 GLU cc_start: 0.8240 (mp0) cc_final: 0.7640 (pm20) REVERT: M 166 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7407 (mt-10) REVERT: M 183 TYR cc_start: 0.8533 (t80) cc_final: 0.8275 (t80) REVERT: N 141 GLU cc_start: 0.7045 (tp30) cc_final: 0.6781 (tp30) outliers start: 24 outliers final: 9 residues processed: 410 average time/residue: 0.1612 time to fit residues: 100.6623 Evaluate side-chains 360 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 351 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain N residue 70 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 196 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 135 HIS ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.137597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.114206 restraints weight = 24509.665| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.33 r_work: 0.3171 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 20776 Z= 0.294 Angle : 0.700 8.168 28063 Z= 0.361 Chirality : 0.047 0.178 3248 Planarity : 0.005 0.042 3640 Dihedral : 7.726 105.602 2933 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.65 % Allowed : 8.11 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.16), residues: 2590 helix: 1.41 (0.14), residues: 1372 sheet: 2.00 (0.29), residues: 259 loop : -0.80 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 173 TYR 0.026 0.003 TYR N 183 PHE 0.015 0.002 PHE A 25 TRP 0.009 0.001 TRP M 174 HIS 0.006 0.001 HIS H 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.29 (20762) covalent geometry : angle 0.70040 / 0.36 (28063) hydrogen bonds : bond 0.04345 / 2.93 ( 1106) hydrogen bonds : angle 4.55750 / 3.17 ( 3528) Misc. bond : bond 0.00140 / 0.07 ( 14) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 364 time to evaluate : 0.535 Fit side-chains REVERT: A 95 TYR cc_start: 0.8598 (t80) cc_final: 0.8335 (t80) REVERT: A 175 ASP cc_start: 0.7375 (t70) cc_final: 0.7112 (m-30) REVERT: A 200 ILE cc_start: 0.8515 (mm) cc_final: 0.8189 (mt) REVERT: B 21 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8193 (mt-10) REVERT: B 161 ARG cc_start: 0.7521 (mtp180) cc_final: 0.7156 (mtp-110) REVERT: B 164 MET cc_start: 0.7616 (ttm) cc_final: 0.7196 (ttt) REVERT: B 175 ASP cc_start: 0.7618 (t70) cc_final: 0.6965 (m-30) REVERT: B 207 ARG cc_start: 0.7543 (ttm-80) cc_final: 0.6810 (ttm-80) REVERT: C 164 MET cc_start: 0.7181 (ttm) cc_final: 0.6857 (ttt) REVERT: C 175 ASP cc_start: 0.7622 (t70) cc_final: 0.6958 (m-30) REVERT: C 200 ILE cc_start: 0.8525 (mm) cc_final: 0.8242 (mt) REVERT: D 87 MET cc_start: 0.7573 (tpp) cc_final: 0.7346 (tpp) REVERT: D 161 ARG cc_start: 0.7601 (mtp180) cc_final: 0.7183 (mtp-110) REVERT: D 164 MET cc_start: 0.7431 (ttm) cc_final: 0.7063 (ttt) REVERT: D 175 ASP cc_start: 0.7261 (t70) cc_final: 0.6886 (m-30) REVERT: D 207 ARG cc_start: 0.7334 (ttm-80) cc_final: 0.6793 (ttm-80) REVERT: E 125 MET cc_start: 0.9034 (mtm) cc_final: 0.8644 (mtm) REVERT: E 135 HIS cc_start: 0.7721 (t-170) cc_final: 0.7465 (t-170) REVERT: E 164 MET cc_start: 0.7167 (ttm) cc_final: 0.6909 (ttt) REVERT: E 175 ASP cc_start: 0.7367 (t70) cc_final: 0.6931 (m-30) REVERT: F 95 TYR cc_start: 0.8584 (t80) cc_final: 0.8353 (t80) REVERT: F 125 MET cc_start: 0.9069 (mtm) cc_final: 0.8534 (mtm) REVERT: F 164 MET cc_start: 0.7465 (ttm) cc_final: 0.7125 (ttt) REVERT: F 175 ASP cc_start: 0.7544 (t70) cc_final: 0.6934 (m-30) REVERT: G 164 MET cc_start: 0.7462 (ttm) cc_final: 0.7099 (ttt) REVERT: G 175 ASP cc_start: 0.7590 (t70) cc_final: 0.6966 (m-30) REVERT: G 207 ARG cc_start: 0.7455 (ttm-80) cc_final: 0.6942 (ttm-80) REVERT: H 150 MET cc_start: 0.7907 (ttt) cc_final: 0.7515 (ttt) REVERT: H 183 TYR cc_start: 0.8750 (t80) cc_final: 0.8377 (t80) REVERT: I 75 MET cc_start: 0.8413 (mmt) cc_final: 0.8179 (mmp) REVERT: I 141 GLU cc_start: 0.7475 (tp30) cc_final: 0.7178 (tp30) REVERT: K 150 MET cc_start: 0.7862 (ttt) cc_final: 0.7516 (ttt) REVERT: L 22 GLU cc_start: 0.8255 (tm-30) cc_final: 0.8019 (tm-30) REVERT: L 141 GLU cc_start: 0.7328 (tp30) cc_final: 0.7117 (tp30) REVERT: M 163 GLU cc_start: 0.8260 (mp0) cc_final: 0.7752 (pm20) REVERT: M 166 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7388 (mt-10) REVERT: N 183 TYR cc_start: 0.8896 (t80) cc_final: 0.8507 (t80) outliers start: 35 outliers final: 25 residues processed: 385 average time/residue: 0.1722 time to fit residues: 97.3489 Evaluate side-chains 349 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 323 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain N residue 70 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 57 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 223 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 206 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.120737 restraints weight = 24039.007| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.30 r_work: 0.3235 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20776 Z= 0.127 Angle : 0.535 5.871 28063 Z= 0.279 Chirality : 0.041 0.167 3248 Planarity : 0.004 0.048 3640 Dihedral : 7.188 107.126 2933 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.70 % Allowed : 9.71 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.16), residues: 2590 helix: 1.78 (0.14), residues: 1379 sheet: 1.96 (0.29), residues: 245 loop : -0.69 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 185 TYR 0.021 0.001 TYR I 183 PHE 0.010 0.001 PHE L 185 TRP 0.006 0.001 TRP M 174 HIS 0.005 0.001 HIS D 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (20762) covalent geometry : angle 0.53510 / 0.28 (28063) hydrogen bonds : bond 0.03107 / 2.11 ( 1106) hydrogen bonds : angle 4.23243 / 2.94 ( 3528) Misc. bond : bond 0.00040 / 0.02 ( 14) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 343 time to evaluate : 0.702 Fit side-chains REVERT: A 175 ASP cc_start: 0.7623 (t70) cc_final: 0.7231 (m-30) REVERT: B 21 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8182 (mt-10) REVERT: B 50 ASP cc_start: 0.7200 (t70) cc_final: 0.6998 (t70) REVERT: B 164 MET cc_start: 0.7453 (ttm) cc_final: 0.7064 (ttt) REVERT: B 175 ASP cc_start: 0.7507 (t70) cc_final: 0.7022 (m-30) REVERT: B 205 GLU cc_start: 0.8093 (pm20) cc_final: 0.7762 (mp0) REVERT: C 164 MET cc_start: 0.7319 (ttm) cc_final: 0.6973 (ttt) REVERT: C 175 ASP cc_start: 0.7539 (t70) cc_final: 0.6950 (m-30) REVERT: C 200 ILE cc_start: 0.8447 (mm) cc_final: 0.8093 (mt) REVERT: D 57 MET cc_start: 0.8295 (mtm) cc_final: 0.8093 (mtm) REVERT: D 164 MET cc_start: 0.7392 (ttm) cc_final: 0.7024 (ttt) REVERT: D 175 ASP cc_start: 0.7355 (t70) cc_final: 0.7001 (m-30) REVERT: D 200 ILE cc_start: 0.8568 (mm) cc_final: 0.8336 (mt) REVERT: E 125 MET cc_start: 0.8933 (mtm) cc_final: 0.8716 (mtp) REVERT: E 135 HIS cc_start: 0.7700 (t-170) cc_final: 0.7476 (t-170) REVERT: E 164 MET cc_start: 0.7183 (ttm) cc_final: 0.6847 (ttt) REVERT: E 175 ASP cc_start: 0.7437 (t70) cc_final: 0.7044 (m-30) REVERT: F 164 MET cc_start: 0.7441 (ttm) cc_final: 0.7154 (ttt) REVERT: F 175 ASP cc_start: 0.7604 (t70) cc_final: 0.7079 (m-30) REVERT: G 50 ASP cc_start: 0.7570 (t70) cc_final: 0.7273 (t70) REVERT: G 164 MET cc_start: 0.7437 (ttm) cc_final: 0.7061 (ttt) REVERT: G 175 ASP cc_start: 0.7613 (t70) cc_final: 0.7065 (m-30) REVERT: G 200 ILE cc_start: 0.8272 (mm) cc_final: 0.7956 (mt) REVERT: G 201 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.7995 (m-30) REVERT: H 150 MET cc_start: 0.8123 (ttt) cc_final: 0.7749 (ttt) REVERT: H 183 TYR cc_start: 0.8748 (t80) cc_final: 0.8392 (t80) REVERT: J 166 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7731 (mt-10) REVERT: J 171 ARG cc_start: 0.6317 (mtp180) cc_final: 0.5808 (ttm170) REVERT: K 171 ARG cc_start: 0.6331 (mtm-85) cc_final: 0.6001 (mtm110) REVERT: M 79 ASP cc_start: 0.7940 (m-30) cc_final: 0.7730 (m-30) REVERT: M 163 GLU cc_start: 0.8292 (mp0) cc_final: 0.7832 (pm20) REVERT: M 166 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7565 (mt-10) REVERT: M 171 ARG cc_start: 0.6631 (mtp180) cc_final: 0.5999 (ttp-110) REVERT: N 171 ARG cc_start: 0.6168 (mtp180) cc_final: 0.5518 (ttm170) outliers start: 36 outliers final: 24 residues processed: 366 average time/residue: 0.1529 time to fit residues: 85.6761 Evaluate side-chains 335 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 309 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 201 ASP Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 95 MET Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 190 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 54 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 chunk 237 optimal weight: 0.8980 chunk 245 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.145351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.121520 restraints weight = 23996.407| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.28 r_work: 0.3252 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20776 Z= 0.123 Angle : 0.523 5.739 28063 Z= 0.273 Chirality : 0.041 0.165 3248 Planarity : 0.004 0.033 3640 Dihedral : 7.005 107.965 2933 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.12 % Allowed : 9.57 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.16), residues: 2590 helix: 2.08 (0.14), residues: 1351 sheet: 1.50 (0.29), residues: 259 loop : -0.69 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 185 TYR 0.021 0.001 TYR I 183 PHE 0.010 0.001 PHE L 185 TRP 0.005 0.001 TRP J 174 HIS 0.004 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (20762) covalent geometry : angle 0.52310 / 0.27 (28063) hydrogen bonds : bond 0.02986 / 2.03 ( 1106) hydrogen bonds : angle 4.12459 / 2.86 ( 3528) Misc. bond : bond 0.00043 / 0.02 ( 14) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 333 time to evaluate : 0.790 Fit side-chains REVERT: A 175 ASP cc_start: 0.7463 (t70) cc_final: 0.7192 (m-30) REVERT: A 201 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7781 (m-30) REVERT: A 207 ARG cc_start: 0.7330 (ttm-80) cc_final: 0.6990 (mtm-85) REVERT: B 164 MET cc_start: 0.7377 (ttm) cc_final: 0.6984 (ttt) REVERT: B 175 ASP cc_start: 0.7644 (t70) cc_final: 0.7050 (m-30) REVERT: C 21 GLU cc_start: 0.7930 (tt0) cc_final: 0.7677 (mt-10) REVERT: C 164 MET cc_start: 0.7319 (ttm) cc_final: 0.6987 (ttt) REVERT: C 175 ASP cc_start: 0.7560 (t70) cc_final: 0.6951 (m-30) REVERT: C 200 ILE cc_start: 0.8440 (mm) cc_final: 0.8109 (mt) REVERT: D 57 MET cc_start: 0.8243 (mtm) cc_final: 0.8026 (mtm) REVERT: D 164 MET cc_start: 0.7252 (ttm) cc_final: 0.6893 (ttt) REVERT: D 175 ASP cc_start: 0.7425 (t70) cc_final: 0.7100 (m-30) REVERT: D 200 ILE cc_start: 0.8545 (mm) cc_final: 0.8317 (mt) REVERT: E 125 MET cc_start: 0.8871 (mtm) cc_final: 0.8651 (mtp) REVERT: E 164 MET cc_start: 0.7142 (ttm) cc_final: 0.6774 (ttt) REVERT: E 175 ASP cc_start: 0.7483 (t70) cc_final: 0.7073 (m-30) REVERT: F 87 MET cc_start: 0.7564 (tpp) cc_final: 0.7232 (tpp) REVERT: F 164 MET cc_start: 0.7361 (ttm) cc_final: 0.7062 (ttt) REVERT: F 175 ASP cc_start: 0.7514 (t70) cc_final: 0.7153 (m-30) REVERT: G 164 MET cc_start: 0.7477 (ttm) cc_final: 0.7108 (ttt) REVERT: G 175 ASP cc_start: 0.7665 (t70) cc_final: 0.7090 (m-30) REVERT: G 200 ILE cc_start: 0.8304 (mm) cc_final: 0.8028 (mt) REVERT: G 201 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7917 (m-30) REVERT: G 205 GLU cc_start: 0.8074 (pm20) cc_final: 0.7678 (tm-30) REVERT: H 183 TYR cc_start: 0.8767 (t80) cc_final: 0.8418 (t80) REVERT: I 22 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: I 166 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7648 (mt-10) REVERT: J 171 ARG cc_start: 0.6347 (mtp180) cc_final: 0.5887 (ttp-110) REVERT: K 150 MET cc_start: 0.7910 (ttt) cc_final: 0.7696 (ttt) REVERT: K 171 ARG cc_start: 0.6246 (mtm-85) cc_final: 0.5929 (mtm110) REVERT: M 163 GLU cc_start: 0.8272 (mp0) cc_final: 0.7795 (pm20) REVERT: M 171 ARG cc_start: 0.6582 (mtp180) cc_final: 0.6016 (ttp-110) REVERT: N 171 ARG cc_start: 0.6268 (mtp180) cc_final: 0.5926 (mtm-85) outliers start: 45 outliers final: 31 residues processed: 362 average time/residue: 0.1519 time to fit residues: 84.9948 Evaluate side-chains 374 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 340 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 201 ASP Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 190 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 138 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 201 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 222 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.146410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.122521 restraints weight = 23996.320| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.29 r_work: 0.3265 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20776 Z= 0.116 Angle : 0.513 5.516 28063 Z= 0.267 Chirality : 0.041 0.163 3248 Planarity : 0.004 0.034 3640 Dihedral : 6.880 108.728 2933 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.93 % Allowed : 10.18 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.16), residues: 2590 helix: 2.19 (0.14), residues: 1351 sheet: 1.48 (0.29), residues: 259 loop : -0.69 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 185 TYR 0.020 0.001 TYR I 183 PHE 0.010 0.001 PHE L 185 TRP 0.007 0.001 TRP I 174 HIS 0.003 0.001 HIS C 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (20762) covalent geometry : angle 0.51296 / 0.27 (28063) hydrogen bonds : bond 0.02856 / 1.94 ( 1106) hydrogen bonds : angle 4.07786 / 2.82 ( 3528) Misc. bond : bond 0.00035 / 0.02 ( 14) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 345 time to evaluate : 0.658 Fit side-chains REVERT: A 175 ASP cc_start: 0.7442 (t70) cc_final: 0.7147 (m-30) REVERT: A 201 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7796 (m-30) REVERT: A 205 GLU cc_start: 0.8074 (pm20) cc_final: 0.7646 (mp0) REVERT: A 207 ARG cc_start: 0.7445 (ttm-80) cc_final: 0.7052 (mtm-85) REVERT: B 164 MET cc_start: 0.7348 (ttm) cc_final: 0.6940 (ttt) REVERT: B 175 ASP cc_start: 0.7456 (t70) cc_final: 0.7070 (m-30) REVERT: B 205 GLU cc_start: 0.7718 (mp0) cc_final: 0.7376 (mp0) REVERT: C 21 GLU cc_start: 0.7957 (tt0) cc_final: 0.7692 (mt-10) REVERT: C 175 ASP cc_start: 0.7568 (t70) cc_final: 0.6940 (m-30) REVERT: C 200 ILE cc_start: 0.8466 (mm) cc_final: 0.8137 (mt) REVERT: D 57 MET cc_start: 0.8253 (mtm) cc_final: 0.8038 (mtm) REVERT: D 164 MET cc_start: 0.7247 (ttm) cc_final: 0.6886 (ttt) REVERT: D 175 ASP cc_start: 0.7424 (t70) cc_final: 0.7115 (m-30) REVERT: D 200 ILE cc_start: 0.8547 (mm) cc_final: 0.8317 (mt) REVERT: E 125 MET cc_start: 0.8862 (mtm) cc_final: 0.8642 (mtp) REVERT: E 164 MET cc_start: 0.7135 (ttm) cc_final: 0.6739 (ttt) REVERT: E 175 ASP cc_start: 0.7528 (t70) cc_final: 0.7110 (m-30) REVERT: F 164 MET cc_start: 0.7358 (ttm) cc_final: 0.7042 (ttt) REVERT: F 175 ASP cc_start: 0.7540 (t70) cc_final: 0.7162 (m-30) REVERT: G 164 MET cc_start: 0.7441 (ttm) cc_final: 0.7047 (ttt) REVERT: G 175 ASP cc_start: 0.7580 (t70) cc_final: 0.7092 (m-30) REVERT: G 200 ILE cc_start: 0.8274 (mm) cc_final: 0.8003 (mt) REVERT: G 201 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7858 (m-30) REVERT: G 205 GLU cc_start: 0.8115 (pm20) cc_final: 0.7670 (tm-30) REVERT: H 171 ARG cc_start: 0.6449 (mtm-85) cc_final: 0.6196 (mtm-85) REVERT: H 183 TYR cc_start: 0.8743 (t80) cc_final: 0.8381 (t80) REVERT: I 79 ASP cc_start: 0.7737 (m-30) cc_final: 0.7511 (m-30) REVERT: J 166 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7863 (mt-10) REVERT: J 171 ARG cc_start: 0.6456 (mtp180) cc_final: 0.5942 (ttp-110) REVERT: J 173 ARG cc_start: 0.7579 (ttt180) cc_final: 0.7300 (ptm160) REVERT: J 183 TYR cc_start: 0.8810 (t80) cc_final: 0.8493 (t80) REVERT: K 150 MET cc_start: 0.8027 (ttt) cc_final: 0.7717 (ttt) REVERT: M 163 GLU cc_start: 0.8262 (mp0) cc_final: 0.7771 (pm20) REVERT: M 171 ARG cc_start: 0.6637 (mtp180) cc_final: 0.6113 (ttp-110) REVERT: N 171 ARG cc_start: 0.6312 (mtp180) cc_final: 0.5692 (ttm170) REVERT: N 172 ASP cc_start: 0.7287 (m-30) cc_final: 0.7046 (m-30) outliers start: 41 outliers final: 34 residues processed: 371 average time/residue: 0.1522 time to fit residues: 87.4139 Evaluate side-chains 363 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 327 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 186 ASP Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 201 ASP Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 190 ILE Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 190 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 250 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 211 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 216 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 221 optimal weight: 0.7980 chunk 186 optimal weight: 0.7980 chunk 67 optimal weight: 0.0010 chunk 113 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.148541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.124580 restraints weight = 23840.550| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.29 r_work: 0.3294 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20776 Z= 0.101 Angle : 0.500 5.337 28063 Z= 0.261 Chirality : 0.040 0.162 3248 Planarity : 0.004 0.036 3640 Dihedral : 6.759 108.756 2933 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.98 % Allowed : 10.42 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.16), residues: 2590 helix: 2.26 (0.14), residues: 1351 sheet: 1.53 (0.29), residues: 259 loop : -0.66 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 185 TYR 0.019 0.001 TYR I 183 PHE 0.010 0.001 PHE L 185 TRP 0.006 0.001 TRP L 174 HIS 0.003 0.001 HIS C 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (20762) covalent geometry : angle 0.50045 / 0.26 (28063) hydrogen bonds : bond 0.02638 / 1.80 ( 1106) hydrogen bonds : angle 4.03457 / 2.79 ( 3528) Misc. bond : bond 0.00025 / 0.01 ( 14) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 347 time to evaluate : 0.761 Fit side-chains REVERT: A 175 ASP cc_start: 0.7440 (t70) cc_final: 0.7107 (m-30) REVERT: A 201 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7761 (m-30) REVERT: A 207 ARG cc_start: 0.7395 (ttm-80) cc_final: 0.7035 (mtm-85) REVERT: B 164 MET cc_start: 0.7344 (ttm) cc_final: 0.6935 (ttt) REVERT: B 175 ASP cc_start: 0.7584 (t70) cc_final: 0.7022 (m-30) REVERT: C 21 GLU cc_start: 0.7912 (tt0) cc_final: 0.7681 (mt-10) REVERT: C 175 ASP cc_start: 0.7572 (t70) cc_final: 0.6945 (m-30) REVERT: C 200 ILE cc_start: 0.8432 (mm) cc_final: 0.8089 (mt) REVERT: D 164 MET cc_start: 0.7185 (ttm) cc_final: 0.6810 (ttt) REVERT: D 175 ASP cc_start: 0.7447 (t70) cc_final: 0.7135 (m-30) REVERT: D 200 ILE cc_start: 0.8578 (mm) cc_final: 0.8337 (mt) REVERT: E 50 ASP cc_start: 0.7538 (t70) cc_final: 0.7168 (t70) REVERT: E 164 MET cc_start: 0.7157 (ttm) cc_final: 0.6751 (ttt) REVERT: E 175 ASP cc_start: 0.7499 (t70) cc_final: 0.7080 (m-30) REVERT: F 21 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8059 (mt-10) REVERT: F 164 MET cc_start: 0.7336 (ttm) cc_final: 0.7006 (ttt) REVERT: F 175 ASP cc_start: 0.7560 (t70) cc_final: 0.7174 (m-30) REVERT: G 164 MET cc_start: 0.7394 (ttm) cc_final: 0.6987 (ttt) REVERT: G 175 ASP cc_start: 0.7606 (t70) cc_final: 0.7112 (m-30) REVERT: G 201 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7781 (m-30) REVERT: G 205 GLU cc_start: 0.8090 (pm20) cc_final: 0.7665 (tm-30) REVERT: H 183 TYR cc_start: 0.8677 (t80) cc_final: 0.8374 (t80) REVERT: I 22 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7631 (tm-30) REVERT: I 79 ASP cc_start: 0.7772 (m-30) cc_final: 0.7516 (m-30) REVERT: J 171 ARG cc_start: 0.6482 (mtp180) cc_final: 0.5948 (ttm170) REVERT: J 183 TYR cc_start: 0.8792 (t80) cc_final: 0.8530 (t80) REVERT: K 150 MET cc_start: 0.7987 (ttt) cc_final: 0.7712 (ttt) REVERT: K 171 ARG cc_start: 0.6400 (mtm-85) cc_final: 0.5873 (ttp-110) REVERT: M 163 GLU cc_start: 0.8309 (mp0) cc_final: 0.7774 (pm20) REVERT: M 171 ARG cc_start: 0.6482 (mtp180) cc_final: 0.6067 (ttp-110) REVERT: M 183 TYR cc_start: 0.8853 (t80) cc_final: 0.8634 (t80) REVERT: N 171 ARG cc_start: 0.6277 (mtp180) cc_final: 0.5761 (ttm170) REVERT: N 172 ASP cc_start: 0.7320 (m-30) cc_final: 0.7077 (m-30) outliers start: 42 outliers final: 30 residues processed: 375 average time/residue: 0.1490 time to fit residues: 87.6541 Evaluate side-chains 372 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 339 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 201 ASP Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 190 ILE Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 190 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 132 optimal weight: 0.8980 chunk 250 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 58 optimal weight: 0.1980 chunk 10 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.152183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128200 restraints weight = 23743.527| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.27 r_work: 0.3337 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20776 Z= 0.094 Angle : 0.491 5.272 28063 Z= 0.256 Chirality : 0.040 0.161 3248 Planarity : 0.004 0.036 3640 Dihedral : 6.634 107.626 2933 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.70 % Allowed : 10.84 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.17), residues: 2590 helix: 2.35 (0.14), residues: 1351 sheet: 0.79 (0.27), residues: 315 loop : -0.49 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 185 TYR 0.019 0.001 TYR I 183 PHE 0.010 0.001 PHE L 185 TRP 0.005 0.001 TRP H 174 HIS 0.003 0.001 HIS D 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 (20762) covalent geometry : angle 0.49136 / 0.26 (28063) hydrogen bonds : bond 0.02515 / 1.72 ( 1106) hydrogen bonds : angle 3.96341 / 2.74 ( 3528) Misc. bond : bond 0.00021 / 0.01 ( 14) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 354 time to evaluate : 0.760 Fit side-chains REVERT: A 175 ASP cc_start: 0.7306 (t70) cc_final: 0.7022 (m-30) REVERT: A 201 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7715 (m-30) REVERT: A 207 ARG cc_start: 0.7367 (ttm-80) cc_final: 0.7163 (ttm110) REVERT: B 164 MET cc_start: 0.7321 (ttm) cc_final: 0.6929 (ttt) REVERT: B 175 ASP cc_start: 0.7453 (t70) cc_final: 0.7075 (m-30) REVERT: C 93 MET cc_start: 0.8566 (mtp) cc_final: 0.8345 (mtp) REVERT: C 135 HIS cc_start: 0.7331 (t-170) cc_final: 0.7081 (t-170) REVERT: C 175 ASP cc_start: 0.7613 (t70) cc_final: 0.6968 (m-30) REVERT: C 200 ILE cc_start: 0.8401 (mm) cc_final: 0.8052 (mt) REVERT: C 201 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7433 (m-30) REVERT: D 164 MET cc_start: 0.7190 (ttm) cc_final: 0.6827 (ttt) REVERT: D 175 ASP cc_start: 0.7397 (t70) cc_final: 0.7086 (m-30) REVERT: E 50 ASP cc_start: 0.7503 (t70) cc_final: 0.7077 (t70) REVERT: E 164 MET cc_start: 0.7080 (ttm) cc_final: 0.6654 (ttt) REVERT: E 175 ASP cc_start: 0.7499 (t70) cc_final: 0.7018 (m-30) REVERT: F 21 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8094 (mt-10) REVERT: F 164 MET cc_start: 0.7348 (ttm) cc_final: 0.7011 (ttt) REVERT: F 175 ASP cc_start: 0.7523 (t70) cc_final: 0.7180 (m-30) REVERT: F 205 GLU cc_start: 0.8208 (pm20) cc_final: 0.7819 (mp0) REVERT: G 175 ASP cc_start: 0.7600 (t70) cc_final: 0.7079 (m-30) REVERT: G 201 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7630 (m-30) REVERT: G 205 GLU cc_start: 0.8104 (pm20) cc_final: 0.7695 (tm-30) REVERT: H 183 TYR cc_start: 0.8661 (t80) cc_final: 0.8405 (t80) REVERT: J 166 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7944 (mt-10) REVERT: J 171 ARG cc_start: 0.6411 (mtp180) cc_final: 0.6074 (mtm110) REVERT: K 150 MET cc_start: 0.8054 (ttt) cc_final: 0.7783 (ttt) REVERT: K 171 ARG cc_start: 0.6223 (mtm-85) cc_final: 0.5789 (ttp-110) REVERT: K 173 ARG cc_start: 0.7255 (ttt180) cc_final: 0.6894 (ptm160) REVERT: M 163 GLU cc_start: 0.8220 (mp0) cc_final: 0.7744 (pm20) REVERT: M 171 ARG cc_start: 0.6388 (mtp180) cc_final: 0.6127 (ttp-110) REVERT: N 171 ARG cc_start: 0.6422 (mtp180) cc_final: 0.5874 (ttm170) REVERT: N 172 ASP cc_start: 0.7561 (m-30) cc_final: 0.7347 (m-30) outliers start: 36 outliers final: 28 residues processed: 377 average time/residue: 0.1529 time to fit residues: 90.0768 Evaluate side-chains 353 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 322 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 201 ASP Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 190 ILE Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain N residue 70 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 100 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 228 optimal weight: 4.9990 chunk 199 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 107 optimal weight: 0.0370 chunk 231 optimal weight: 2.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.146536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.122602 restraints weight = 24333.514| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.29 r_work: 0.3263 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20776 Z= 0.151 Angle : 0.549 6.537 28063 Z= 0.284 Chirality : 0.042 0.181 3248 Planarity : 0.004 0.035 3640 Dihedral : 6.809 108.380 2933 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.60 % Allowed : 11.50 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.16), residues: 2590 helix: 2.22 (0.14), residues: 1351 sheet: 1.04 (0.27), residues: 301 loop : -0.64 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 185 TYR 0.025 0.002 TYR I 183 PHE 0.017 0.001 PHE L 185 TRP 0.008 0.001 TRP J 174 HIS 0.005 0.001 HIS C 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (20762) covalent geometry : angle 0.54931 / 0.28 (28063) hydrogen bonds : bond 0.03113 / 2.11 ( 1106) hydrogen bonds : angle 4.12652 / 2.85 ( 3528) Misc. bond : bond 0.00060 / 0.03 ( 14) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 330 time to evaluate : 0.943 Fit side-chains REVERT: A 175 ASP cc_start: 0.7403 (t70) cc_final: 0.7075 (m-30) REVERT: A 201 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7874 (m-30) REVERT: A 207 ARG cc_start: 0.7561 (ttm-80) cc_final: 0.7135 (ttm-80) REVERT: B 164 MET cc_start: 0.7370 (ttm) cc_final: 0.6984 (ttt) REVERT: B 175 ASP cc_start: 0.7525 (t70) cc_final: 0.7120 (m-30) REVERT: C 175 ASP cc_start: 0.7640 (t70) cc_final: 0.6990 (m-30) REVERT: C 200 ILE cc_start: 0.8528 (mm) cc_final: 0.8208 (mt) REVERT: C 201 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7512 (m-30) REVERT: D 57 MET cc_start: 0.8280 (mtm) cc_final: 0.8059 (mtm) REVERT: D 161 ARG cc_start: 0.7594 (mtp180) cc_final: 0.7319 (mtp-110) REVERT: D 164 MET cc_start: 0.7383 (ttm) cc_final: 0.6995 (ttt) REVERT: D 175 ASP cc_start: 0.7495 (t70) cc_final: 0.7177 (m-30) REVERT: D 207 ARG cc_start: 0.7512 (ttm-80) cc_final: 0.7179 (ttm-80) REVERT: E 125 MET cc_start: 0.8707 (mtt) cc_final: 0.8369 (mtm) REVERT: E 164 MET cc_start: 0.7156 (ttm) cc_final: 0.6749 (ttt) REVERT: E 175 ASP cc_start: 0.7678 (t70) cc_final: 0.7168 (m-30) REVERT: F 164 MET cc_start: 0.7413 (ttm) cc_final: 0.7074 (ttt) REVERT: F 175 ASP cc_start: 0.7663 (t70) cc_final: 0.7277 (m-30) REVERT: F 205 GLU cc_start: 0.8307 (pm20) cc_final: 0.7836 (tp30) REVERT: G 175 ASP cc_start: 0.7675 (t70) cc_final: 0.7116 (m-30) REVERT: G 201 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.7986 (m-30) REVERT: G 205 GLU cc_start: 0.8157 (pm20) cc_final: 0.7693 (tm-30) REVERT: H 183 TYR cc_start: 0.8793 (t80) cc_final: 0.8502 (t80) REVERT: I 171 ARG cc_start: 0.6588 (mtp180) cc_final: 0.6121 (ttp-110) REVERT: J 95 MET cc_start: 0.8633 (ttp) cc_final: 0.8409 (ttp) REVERT: J 171 ARG cc_start: 0.6520 (mtp180) cc_final: 0.6297 (mtm-85) REVERT: K 150 MET cc_start: 0.8057 (ttt) cc_final: 0.7761 (ttt) REVERT: K 171 ARG cc_start: 0.6367 (mtm-85) cc_final: 0.5868 (ttp-110) REVERT: M 99 MET cc_start: 0.8703 (mmm) cc_final: 0.8183 (tpt) REVERT: M 163 GLU cc_start: 0.8225 (mp0) cc_final: 0.7739 (pm20) REVERT: M 171 ARG cc_start: 0.6452 (mtp180) cc_final: 0.6028 (ttp-110) REVERT: N 171 ARG cc_start: 0.6500 (mtp180) cc_final: 0.6199 (mtm-85) outliers start: 34 outliers final: 31 residues processed: 352 average time/residue: 0.1520 time to fit residues: 83.4836 Evaluate side-chains 358 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 324 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 201 ASP Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain J residue 190 ILE Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 70 SER Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 190 ILE Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 190 ILE Chi-restraints excluded: chain N residue 70 SER Chi-restraints excluded: chain N residue 190 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 109 optimal weight: 0.9990 chunk 183 optimal weight: 8.9990 chunk 174 optimal weight: 7.9990 chunk 188 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 211 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 chunk 231 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 209 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.145948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.121913 restraints weight = 24041.713| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.30 r_work: 0.3264 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20776 Z= 0.130 Angle : 0.532 6.253 28063 Z= 0.276 Chirality : 0.042 0.172 3248 Planarity : 0.004 0.057 3640 Dihedral : 6.805 108.759 2933 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.65 % Allowed : 11.36 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.55 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.16), residues: 2590 helix: 2.23 (0.14), residues: 1351 sheet: 1.00 (0.27), residues: 301 loop : -0.67 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 185 TYR 0.023 0.001 TYR I 183 PHE 0.019 0.001 PHE L 185 TRP 0.007 0.001 TRP J 174 HIS 0.003 0.001 HIS C 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (20762) covalent geometry : angle 0.53189 / 0.28 (28063) hydrogen bonds : bond 0.02923 / 1.99 ( 1106) hydrogen bonds : angle 4.11249 / 2.84 ( 3528) Misc. bond : bond 0.00046 / 0.02 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4018.25 seconds wall clock time: 69 minutes 57.26 seconds (4197.26 seconds total)